Hi Chetan, try to use the <configfile> feature to create file4.txt ...
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cconfigfiles.3E_tag_set Cheers, Bjoern Am 04.03.2014 15:04, schrieb do kadya:
Respected Sir / Ma'am, 'x' tool having 3 commands, 1) command takes files from path. ex perl x.pl --mode 1 file1.bam file2.bam file3.fasta --output result1.txt 2) file4 must have name of result1.txt, file1.bam, file2.bam perl x.pl --mode 2 file4.txt --output-directory ~/result2/ for this second command how can i tell galaxy that i need to see the output file name and other 2 bam file name inside single text file. whenever I try to run this command it says file not found. I am uploading bam files by linking galaxy to that file hence when I specify full path, file1.bam and file2.bam are found. But I need result of 1st command. I want its file name in file4.txt How can I do this in galaxy ? Waiting for positive reply. Thank You. -- Chetan ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
